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Sample GSM1701702 Query DataSets for GSM1701702
Status Public on Aug 01, 2015
Title RPL_yeast_ligase
Sample type SRA
 
Source name S. cerevisiae strain FY
Organism Saccharomyces cerevisiae
Characteristics strain: FY
Treatment protocol Cells were treated in situ using the RPL protocol as described in the associated manuscript
Growth protocol GM12878 were grown at 37 in RPMI-1640 containing 15% FBS, 1X Anti-Anti, and 1X Plasmocin; FY were struck out on YPD plates and grown at 30
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIZol and Zymo DirectZOL columns
Illumina TruSeq
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Adapter trimming and read fusion of mate-pairs by SeqPrep
Alignment via STAR/2.4.0 (following parameters:
Processing of STAR intron calls using custom bash/python scripts provided with manuscript
Genome_build: hg19 / SacCer3
Supplementary_files_format_and_content: "Pairs" files that document coordinates of ligation junctions between/within molecular species
 
Submission date Jun 02, 2015
Last update date May 15, 2019
Contact name Vijay Ramani
Organization name UCSF
Department Biochemistry & Biophysics
Lab Ramani Lab
Street address 600 16th St, GH-S312B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL13821
Series (1)
GSE69472 RNA Proximity Ligation to Resolve Intramolecular RNA Structures in situ
Relations
BioSample SAMN03755635
SRA SRX1046447

Supplementary file Size Download File type/resource
GSM1701702_RPL_yeast_ligase.pairs.txt.gz 4.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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